[Xplor-nih] Torsion angle dynamics

[Charles at Schwieters.org]

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Hello Lei--

>      I am using internal dynamics in my annealing (IVM) protocol.  
> However,I still see in my output, the angle and bond terms are still  
> changing dramatically. According to the algorithm, these energies  
> should not change so much.  In the test file in eginput/protG/ 
> anneal.py.out, the energies does not drift so much.I am wondering  
> where the problem is and how the program works when they group atoms  
> together in torsion angle dynamics.  I attached part of my output  
> below. I really appreciate it if you can take a look at it.

Looking at your output I see that you have cycle links which the IVM
broke in order to do torsion angle dynamics. These broken links
correspond to bonds which are not constrained to remain fixed:

> > AT_Build::buildNode: cycle link found between atoms 109 TYR 7 CD2  
> > and 106
> > TYR 7 CG
> >         removing bond.

I wonder why these cycles exist. Do you have modified residues? Or some
nonstandard IVM setup?

>      Besides, I keep seeing warnings like "Ran out of space.  
> RESIZING", any idea what is going on? Is it likely a problem?

These are informational messages from the nonbonded energy term and can
be safely ignored.

best regards--
Charles
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